Main
Yan Shi HU (胡言石)
I graduated from the Bioinformatics PhD program at Zhejiang University. My main interests lie in bioinformatics, computational systems biology, and molecular mechanisms related to major complex diseases. Currently I am deeply fascinated by decyphering large-scale disease comorbidity patterns and detailed disease comorbidity between Parkinson's and Crohn's disease.
I have authored 12 SCI papers, which have garnered extensive attention from academic communities and been widely cited by articles published in high-impact journals such as Science, Gastroenterology, Pharmacological Reviews, Trends in Neurosciences, Trends in Cancer, Alzheimer's & Dementia, Trends in Genetics, Brain and Nucleic Acids Research. Currently I serve as (ad hoc) peer reviewer for 17 SCI journals.Research Interests:
Machine Learning/Deep Learning/AI4BioMed | NetMed/NetBio | Neuroscience
WORKING EXPERIENCE
Research Associate
College of Life Sciences
Zhejiang University
Hangzhou, China
2024 - 2023
Research Assistant
School of Biomedical Engineering
Tianjin Medical University
Tianjin, China
2017 - 2016
EDUCATION
Doctor of Philosophy in Bioinformatics
Zhejiang University
Hangzhou, China
- Dissertation: Systems biology analyses of molecular mechanisms underlying comorbidity between Parkinson's and Crohn's disease
- Adviser: Prof. Ming Chen (陈铭)
2023 - 2017
Master of Philosophy in Biomedical Engineering
Tianjin Medical University
Tianjin, China
2016 - 2013
- Dissertation: Biochemical pathway and protein-protein interaction network based analyses of genes associated with Parkinson's disease
- Adviser: Prof. Ju Wang (王举)
Bachelor of Science in Biomedical Engineering
Shandong First Medical University
Shandong Academy of Medical Sciences
Taian, China
2013 - 2009
- Dissertation: Comparative study of three MATLAB based methods for retinal image brightness and contrast adjustment
- Adviser: Prof. Yongxin Guo (郭永新)
ACADEMIC HONORS & AWARDS
Bioinformatics Society of Zhejiang Province of China, Member
Bioinformatics Society of Zhejiang Province of China
N/A
now - 2017
Zhejiang University Award of Honor for Graduate
Zhejiang University
N/A
2019
Zhejiang University First-Class Scholarship for Doctoral Mid-term Examination
Zhejiang University
Scholarship amount: ¥ 20,000
N/A
2018
Zhejiang University Award of Honor for Graduate
Zhejiang University
N/A
Zhejiang University Excellent Doctoral Freshman Scholarship
Zhejiang University
Scholarship amount: ¥ 10,000
N/A
2017
Second-Class Prize for Excellent Poster
The 6th National Conference on Bioinformatics & Systems Biology of China (第六届全国生物信息学与系统生物学学术大会)
Prize amount: ¥ 400
N/A
2014
Shandong First Medical University Excellent Undergraduate Thesis Award
Shandong First Medical University
Shandong Academy of Medical Sciences
N/A
2013
Shandong First Medical University Second-Class Scholarship
Shandong First Medical University
Shandong Academy of Medical Sciences
N/A
2011
Shandong First Medical University Third-Class Scholarship
Shandong First Medical University
Shandong Academy of Medical Sciences
N/A
2010
SCI JOURNAL REFEREE
Science China-Life Sciences
Impact Factor: 8.0
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# 1
Bioinformatics
Impact Factor: 7.6
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# 2
International Journal of Intelligent Systems
Impact Factor: 5.9
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# 3
Molecular Neurobiology
Impact Factor: 5.1
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# 4
Frontiers in Neuroscience
Impact Factor: 4.3
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# 5
Scientific Reports
Impact Factor: 4.3
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# 6
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Impact Factor: 3.6
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# 7
Frontiers in Neurology
Impact Factor: 3.3
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# 8
PLOS ONE
Impact Factor: 3.3
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# 9
Journal of Molecular Neuroscience
Impact Factor: 2.8
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# 10
Mammalian Genome
Impact Factor: 2.7
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# 11
Computational Biology and Chemistry
Impact Factor: 2.6
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# 12
BMC Medical Genomics
Impact Factor: 2.5
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# 13
BMC Neurology
Impact Factor: 2.5
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# 14
Current Bioinformatics
Impact Factor: 2.4
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# 15
Cell Biochemistry and Biophysics
Impact Factor: 2.0
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# 16
BMC Genomic Data
Impact Factor: 1.9
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# 17
PUBLICATIONS & PREPRINTS
Decrypting human biological pathway crosstalk landscape in a deep learning architecture
To Appear on bioRχiv.
N/A
2024
YS Hu#, Y Chen#, Y Hu, M Chen*
AWmeta empowers adaptively-weighted meta-analysis for gene expression data
To Appear on bioRχiv.
N/A
N/A
YS Hu, Y Hu, M Chen*
Systems biology framework unravels molecular substrates underlying comorbidity between Parkinson's and Crohn's disease
To Appear on medRχiv.
N/A
N/A
YS Hu, B She, Z Yin, X Yu, W Wu, M Chen*
Benchmarking alternative polyadenylation detection in single-cell and spatial transcriptomes
bioRχiv. 2024.10.15.618405.
Submitted to Genome Biology
Impact Factor: 16.5
N/A
S Li, Z Wang, YS Hu, Q Ni, C Feng, Y Hu, S Zhang, M Chen*
ncPlantDB: A plant ncRNA database with potential ncPEP information and cell type-specific interaction
Nucleic Acids Research. 2024, gkae1017.
Impact Factor: 16.6
N/A
L Liu#, E Liu#, Y Hu, S Li, S Zhang, H Chao, YS Hu, Y Zhu, Y Chen, L Xie, Y Shen, L Wu, M Chen*
Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition
BMC Biology. 2024, 22(1):143.
Impact Factor: 5.4
N/A
C Feng#, RX Tie#, SG Xin#, YH Chen, SD Li, YF Chen, XT Hu, YC Zhou, YJ Liu, YM Hu, YS Hu, H Pan, ZX Wu, HY Chao, SL Zhang, QY Ni, J Huang, W Luo*, H Huang*, M Chen*
HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses
Scientific Data. 2023, 10(1):851.
Impact Factor: 8.9
2023
Z Wu#, C Feng#, YS Hu, Y Zhou, S Li, S Zhang, Y Hu, Y Chen, H Chao, Q Ni, M Chen*
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure
Bioinformatics. 2022, 38(18):4380-4386.
Impact Factor: 7.6
2022
Y Chen#, YS Hu#, X Hu, C Feng, M Chen*
CoVM2: Molecular Biological Data Integration of SARS-CoV-2 Proteins in a Macro-to-Micro Method
Biomolecules. 2022, 12(8):1067.
Impact Factor: 5.4
N/A
H Chen, X Hu, YS Hu, J Zhou, M Chen*
LBD: a manually curated database of experimentally validated lymphoma biomarkers
Database. 2022, Volume 2022, baac051.
Impact Factor: 4.2
N/A
B Tan, S Xin, YS Hu, C Feng*, M Chen*
PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants
Database. 2020, Volume 2020, baaa001.
Impact Factor: 4.2
2020
W Wu, Y Wu, D Hu, Y Zhou, YS Hu, Y Chen, M Chen*
The inflammatory cytokine IL-6 induces FRA1 deacetylation promoting colorectal cancer stemness and malignancy
Oncogene. 2019, 38:4932-4947.
Impact Factor: 7.5
2019
T Wang, P Song, T Zhong, X Wang, X Xiang, Q Liu, H Chen, T Xia, H Liu, Y Niu, YS Hu, L Xu, Y Shao, L Zhu, H Qi, J Shen, T Hou, R Fodde*, J Shao*
Network and Pathway-Based Analyses of Genes Associated with Parkinson’s Disease
Molecular Neurobiology. 2017, 54(6):4452-4465.
Impact Factor: 5.1
N/A
YS Hu, Z Pan, Y Hu, L Zhang*, J Wang*
Detecting pathway relationship in the context of human protein-protein interaction network and its application to Parkinson’s disease
Methods. 2017, 131:93-103.
Impact Factor: 4.2
N/A
Y Hu, Y Yang, Z Fang, YS Hu, L Zhang*, J Wang*
GRONS: a comprehensive genetic resource of nicotine and smoking
Database. 2017, Volume 2017, bax097.
Impact Factor: 4.2
N/A
Z Fang, Y Yang, YS Hu, MD Li*, J Wang*
CONFERENCE PROCEEDINGS
Network and pathway based analyses of genes associated with Parkinson’s disease
The 7th National Conference on Bioinformatics and Systems Biology of China
Chengdu, China
2016
Uncovering the common pathogenesis in neurodegenerative and psychiatric disorder via network approaches
The 7th National Conference on Bioinformatics and Systems Biology of China
Chengdu, China
N/A
Common characteristics of Alzheimer’s disease and Parkinson’s disease based on AlzGene and PDGene databases
The 6th National Conference on Bioinformatics and Systems Biology of China
Nanjing, China
2014
Computing the phenotype similarity based on OMIM database and MESH vocabulary
The 6th National Conference on Bioinformatics and Systems Biology of China
Nanjing, China
N/A
TarPriGO: a new method to prioritize miRNA targets based on Gene Ontology
The 6th National Conference on Bioinformatics and Systems Biology of China
Nanjing, China
N/A
A comprehensive pathway and network analysis of candidate genes associated with nicotine addiction
The 6th National Conference on Bioinformatics and Systems Biology of China
Nanjing, China
N/A
The functional divergence analysis of neuronal nicotinic acetylcholine receptor subunits
The 6th National Conference on Bioinformatics and Systems Biology of China
Nanjing, China
N/A
ACADEMIC TALKS
Zhejiang University-Bielefeld University Joint Symposium
Talk Title: Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach
Bielefeld, Germany
2019
First Sino-Russian Workshop on Integrative Bioinformatics and Systems Biology (WIBSB-2018)
Talk Title: Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach
Novosibirsk, Russia
2018
ACADEMIC POSTERS
Network and pathway based analyses of genes associated with Parkinson’s disease
The 7th National Conference on Bioinformatics and Systems Biology of China
Chengdu, China
2016
Common characteristics of Alzheimer’s disease and Parkinson’s disease based on AlzGene and PDGene databases
The 6th National Conference on Bioinformatics and Systems Biology of China
Nanjing, China
2014
PATENTS
一种生化通路串话识别方法 (Chinese Patent)
Inventor: 陈铭,胡言石,陈俞皓
Application Number: 2023107816823
Filing Date: 2023-06-28
Publication number: CN116959588A
Publication Date: 2023-10-27
N/A
2023
